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Crystal structure of adenylosuccinate lyase from francisella tularensis complexed with fumaric acid
Analyse Crystal structure of adenylosuccinate lyase from francisella tularensis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HW2
- Type
- protein
- Length
- 1,674 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate lyase
- EC
- 4.3.2.2
- UniProt
- Q5NIQ1
- Ligands
- FUM, K, PO4
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 419 | 65% helix, 5% strand | Q5NIQ1 |
| B | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 416 | 62% helix, 5% strand | Q5NIQ1 |
| C | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 422 | 64% helix, 5% strand | Q5NIQ1 |
| D | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 417 | 64% helix, 5% strand | Q5NIQ1 |
Ligands and binding sites
- FUM · Fumaric acid · ligand · 3 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.83 | 0.84 | 120 | FUM, PO4 |
| 2 | 125 | 0.80 | 0.98 | 19 | empty |
| 3 | 870 | 0.80 | 0.82 | 102 | FUM, EDO, PO4 |
| 4 | 118 | 0.79 | 0.98 | 22 | empty |
| 5 | 133 | 0.79 | 0.97 | 30 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3944 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 3687 Ų buried · 59 hydrogen bonds · protein-protein
- B–C · 2044 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1907 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1051 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5HW2 · Crystal Structure of Adenylosuccinate Lyase from Francisella tularensis Complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q5NIQ1
- Elsewhere: RCSB PDB 5HW2 · PDBe 5HW2 · UniProt Q5NIQ1
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